<!doctype html>
<html>
<head>
<meta charset='UTF-8'><meta name='viewport' content='width=device-width initial-scale=1'>
<title>gopAga2.0 Annotation</title><link href='https://fonts.loli.net/css?family=Open+Sans:400italic,700italic,700,400&subset=latin,latin-ext' rel='stylesheet' type='text/css' /><style type='text/css'>html {overflow-x: initial !important;}:root { --bg-color: #ffffff; --text-color: #333333; --select-text-bg-color: #B5D6FC; --select-text-font-color: auto; --monospace: "Lucida Console",Consolas,"Courier",monospace; }
html { font-size: 14px; background-color: var(--bg-color); color: var(--text-color); font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; -webkit-font-smoothing: antialiased; }
body { margin: 0px; padding: 0px; height: auto; bottom: 0px; top: 0px; left: 0px; right: 0px; font-size: 1rem; line-height: 1.42857143; overflow-x: hidden; background-image: inherit; background-size: inherit; background-attachment: inherit; background-origin: inherit; background-clip: inherit; background-color: inherit; tab-size: 4; background-position: inherit inherit; background-repeat: inherit inherit; }
iframe { margin: auto; }
a.url { word-break: break-all; }
a:active, a:hover { outline: 0px; }
.in-text-selection, ::selection { text-shadow: none; background: var(--select-text-bg-color); color: var(--select-text-font-color); }
#write { margin: 0px auto; height: auto; width: inherit; word-break: normal; word-wrap: break-word; position: relative; white-space: normal; overflow-x: visible; padding-top: 40px; }
#write.first-line-indent p { text-indent: 2em; }
#write.first-line-indent li p, #write.first-line-indent p * { text-indent: 0px; }
#write.first-line-indent li { margin-left: 2em; }
.for-image #write { padding-left: 8px; padding-right: 8px; }
body.typora-export { padding-left: 30px; padding-right: 30px; }
.typora-export .footnote-line, .typora-export li, .typora-export p { white-space: pre-wrap; }
@media screen and (max-width: 500px) { 
  body.typora-export { padding-left: 0px; padding-right: 0px; }
  #write { padding-left: 20px; padding-right: 20px; }
  .CodeMirror-sizer { margin-left: 0px !important; }
  .CodeMirror-gutters { display: none !important; }
}
#write li > figure:last-child { margin-bottom: 0.5rem; }
#write ol, #write ul { position: relative; }
img { max-width: 100%; vertical-align: middle; }
button, input, select, textarea { color: inherit; font-family: inherit; font-size: inherit; font-style: inherit; font-variant-caps: inherit; font-weight: inherit; font-stretch: inherit; line-height: inherit; }
input[type="checkbox"], input[type="radio"] { line-height: normal; padding: 0px; }
*, ::after, ::before { box-sizing: border-box; }
#write h1, #write h2, #write h3, #write h4, #write h5, #write h6, #write p, #write pre { width: inherit; }
#write h1, #write h2, #write h3, #write h4, #write h5, #write h6, #write p { position: relative; }
h1, h2, h3, h4, h5, h6 { break-after: avoid-page; break-inside: avoid; orphans: 2; }
p { orphans: 4; }
h1 { font-size: 2rem; }
h2 { font-size: 1.8rem; }
h3 { font-size: 1.6rem; }
h4 { font-size: 1.4rem; }
h5 { font-size: 1.2rem; }
h6 { font-size: 1rem; }
.md-math-block, .md-rawblock, h1, h2, h3, h4, h5, h6, p { margin-top: 1rem; margin-bottom: 1rem; }
.hidden { display: none; }
.md-blockmeta { color: rgb(204, 204, 204); font-weight: 700; font-style: italic; }
a { cursor: pointer; }
sup.md-footnote { padding: 2px 4px; background-color: rgba(238, 238, 238, 0.701961); color: rgb(85, 85, 85); border-top-left-radius: 4px; border-top-right-radius: 4px; border-bottom-right-radius: 4px; border-bottom-left-radius: 4px; cursor: pointer; }
sup.md-footnote a, sup.md-footnote a:hover { color: inherit; text-transform: inherit; text-decoration: inherit; }
#write input[type="checkbox"] { cursor: pointer; width: inherit; height: inherit; }
figure { overflow-x: auto; margin: 1.2em 0px; max-width: calc(100% + 16px); padding: 0px; }
figure > table { margin: 0px !important; }
tr { break-inside: avoid; break-after: auto; }
thead { display: table-header-group; }
table { border-collapse: collapse; border-spacing: 0px; width: 100%; overflow: auto; break-inside: auto; text-align: left; }
table.md-table td { min-width: 32px; }
.CodeMirror-gutters { border-right-width: 0px; background-color: inherit; }
.CodeMirror-linenumber { }
.CodeMirror { text-align: left; }
.CodeMirror-placeholder { opacity: 0.3; }
.CodeMirror pre { padding: 0px 4px; }
.CodeMirror-lines { padding: 0px; }
div.hr:focus { cursor: none; }
#write pre { white-space: pre-wrap; }
#write.fences-no-line-wrapping pre { white-space: pre; }
#write pre.ty-contain-cm { white-space: normal; }
.CodeMirror-gutters { margin-right: 4px; }
.md-fences { font-size: 0.9rem; display: block; break-inside: avoid; text-align: left; overflow: visible; white-space: pre; background-image: inherit; background-size: inherit; background-attachment: inherit; background-origin: inherit; background-clip: inherit; background-color: inherit; position: relative !important; background-position: inherit inherit; background-repeat: inherit inherit; }
.md-diagram-panel { width: 100%; margin-top: 10px; text-align: center; padding-top: 0px; padding-bottom: 8px; overflow-x: auto; }
#write .md-fences.mock-cm { white-space: pre-wrap; }
.md-fences.md-fences-with-lineno { padding-left: 0px; }
#write.fences-no-line-wrapping .md-fences.mock-cm { white-space: pre; overflow-x: auto; }
.md-fences.mock-cm.md-fences-with-lineno { padding-left: 8px; }
.CodeMirror-line, twitterwidget { break-inside: avoid; }
.footnotes { opacity: 0.8; font-size: 0.9rem; margin-top: 1em; margin-bottom: 1em; }
.footnotes + .footnotes { margin-top: 0px; }
.md-reset { margin: 0px; padding: 0px; border: 0px; outline: 0px; vertical-align: top; text-decoration: none; text-shadow: none; float: none; position: static; width: auto; height: auto; white-space: nowrap; cursor: inherit; line-height: normal; font-weight: 400; text-align: left; box-sizing: content-box; direction: ltr; background-position: 0px 0px; background-repeat: initial initial; }
li div { padding-top: 0px; }
blockquote { margin: 1rem 0px; }
li .mathjax-block, li p { margin: 0.5rem 0px; }
li { margin: 0px; position: relative; }
blockquote > :last-child { margin-bottom: 0px; }
blockquote > :first-child, li > :first-child { margin-top: 0px; }
.footnotes-area { color: rgb(136, 136, 136); margin-top: 0.714rem; padding-bottom: 0.143rem; white-space: normal; }
#write .footnote-line { white-space: pre-wrap; }
@media print { 
  body, html { border: 1px solid transparent; height: 99%; break-after: avoid-page; break-before: avoid-page; }
  #write { margin-top: 0px; padding-top: 0px; border-color: transparent !important; }
  .typora-export * { -webkit-print-color-adjust: exact; }
  html.blink-to-pdf { font-size: 13px; }
  .typora-export #write { padding-left: 32px; padding-right: 32px; padding-bottom: 0px; break-after: avoid-page; }
  .typora-export #write::after { height: 0px; }
  @page { margin: 20mm 0px; }
}
.footnote-line { margin-top: 0.714em; font-size: 0.7em; }
a img, img a { cursor: pointer; }
pre.md-meta-block { font-size: 0.8rem; min-height: 0.8rem; white-space: pre-wrap; background-color: rgb(204, 204, 204); display: block; overflow-x: hidden; background-position: initial initial; background-repeat: initial initial; }
p > .md-image:only-child:not(.md-img-error) img, p > img:only-child { display: block; margin: auto; }
p > .md-image:only-child { display: inline-block; width: 100%; }
#write .MathJax_Display { margin: 0.8em 0px 0px; }
.md-math-block { width: 100%; }
.md-math-block:not(:empty)::after { display: none; }
[contenteditable="true"]:active, [contenteditable="true"]:focus { outline: 0px; box-shadow: none; }
.md-task-list-item { position: relative; list-style-type: none; }
.task-list-item.md-task-list-item { padding-left: 0px; }
.md-task-list-item > input { position: absolute; top: 0px; left: 0px; margin-left: -1.2em; margin-top: calc(1em - 10px); border: none; }
.math { font-size: 1rem; }
.md-toc { min-height: 3.58rem; position: relative; font-size: 0.9rem; border-top-left-radius: 10px; border-top-right-radius: 10px; border-bottom-right-radius: 10px; border-bottom-left-radius: 10px; }
.md-toc-content { position: relative; margin-left: 0px; }
.md-toc-content::after, .md-toc::after { display: none; }
.md-toc-item { display: block; color: rgb(65, 131, 196); }
.md-toc-item a { text-decoration: none; }
.md-toc-inner:hover { text-decoration: underline; }
.md-toc-inner { display: inline-block; cursor: pointer; }
.md-toc-h1 .md-toc-inner { margin-left: 0px; font-weight: 700; }
.md-toc-h2 .md-toc-inner { margin-left: 2em; }
.md-toc-h3 .md-toc-inner { margin-left: 4em; }
.md-toc-h4 .md-toc-inner { margin-left: 6em; }
.md-toc-h5 .md-toc-inner { margin-left: 8em; }
.md-toc-h6 .md-toc-inner { margin-left: 10em; }
@media screen and (max-width: 48em) { 
  .md-toc-h3 .md-toc-inner { margin-left: 3.5em; }
  .md-toc-h4 .md-toc-inner { margin-left: 5em; }
  .md-toc-h5 .md-toc-inner { margin-left: 6.5em; }
  .md-toc-h6 .md-toc-inner { margin-left: 8em; }
}
a.md-toc-inner { font-size: inherit; font-style: inherit; font-weight: inherit; line-height: inherit; }
.footnote-line a:not(.reversefootnote) { color: inherit; }
.md-attr { display: none; }
.md-fn-count::after { content: "."; }
code, pre, samp, tt { font-family: var(--monospace); }
kbd { margin: 0px 0.1em; padding: 0.1em 0.6em; font-size: 0.8em; color: rgb(36, 39, 41); background-color: rgb(255, 255, 255); border: 1px solid rgb(173, 179, 185); border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; box-shadow: rgba(12, 13, 14, 0.2) 0px 1px 0px, rgb(255, 255, 255) 0px 0px 0px 2px inset; white-space: nowrap; vertical-align: middle; background-position: initial initial; background-repeat: initial initial; }
.md-comment { color: rgb(162, 127, 3); opacity: 0.8; font-family: var(--monospace); }
code { text-align: left; }
a.md-print-anchor { white-space: pre !important; border: none !important; display: inline-block !important; position: absolute !important; width: 1px !important; right: 0px !important; outline: 0px !important; text-shadow: initial !important; background-position: 0px 0px !important; background-repeat: initial initial !important; }
.md-inline-math .MathJax_SVG .noError { display: none !important; }
.html-for-mac .inline-math-svg .MathJax_SVG { vertical-align: 0.2px; }
.md-math-block .MathJax_SVG_Display { text-align: center; margin: 0px; position: relative; text-indent: 0px; max-width: none; max-height: none; min-height: 0px; min-width: 100%; width: auto; overflow-y: hidden; display: block !important; }
.MathJax_SVG_Display, .md-inline-math .MathJax_SVG_Display { width: auto; margin: inherit; display: inline-block !important; }
.MathJax_SVG .MJX-monospace { font-family: var(--monospace); }
.MathJax_SVG .MJX-sans-serif { font-family: sans-serif; }
.MathJax_SVG { display: inline; font-style: normal; font-weight: 400; line-height: normal; zoom: 90%; text-indent: 0px; text-align: left; text-transform: none; letter-spacing: normal; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px; margin: 0px; }
.MathJax_SVG * { transition: none; }
.MathJax_SVG_Display svg { vertical-align: middle !important; margin-bottom: 0px !important; }
.os-windows.monocolor-emoji .md-emoji { font-family: "Segoe UI Symbol", sans-serif; }
.md-diagram-panel > svg { max-width: 100%; }
[lang="mermaid"] svg, [lang="flow"] svg { max-width: 100%; }
[lang="mermaid"] .node text { font-size: 1rem; }
table tr th { border-bottom-width: 0px; }
video { max-width: 100%; display: block; margin: 0px auto; }
iframe { max-width: 100%; width: 100%; border: none; }
.highlight td, .highlight tr { border: 0px; }


.CodeMirror { height: auto; }
.CodeMirror.cm-s-inner { background-image: inherit; background-size: inherit; background-attachment: inherit; background-origin: inherit; background-clip: inherit; background-color: inherit; background-position: inherit inherit; background-repeat: inherit inherit; }
.CodeMirror-scroll { overflow-y: hidden; overflow-x: auto; z-index: 3; }
.CodeMirror-gutter-filler, .CodeMirror-scrollbar-filler { background-color: rgb(255, 255, 255); }
.CodeMirror-gutters { border-right-width: 1px; border-right-style: solid; border-right-color: rgb(221, 221, 221); background-image: inherit; background-size: inherit; background-attachment: inherit; background-origin: inherit; background-clip: inherit; background-color: inherit; white-space: nowrap; background-position: inherit inherit; background-repeat: inherit inherit; }
.CodeMirror-linenumber { padding: 0px 3px 0px 5px; text-align: right; color: rgb(153, 153, 153); }
.cm-s-inner .cm-keyword { color: rgb(119, 0, 136); }
.cm-s-inner .cm-atom, .cm-s-inner.cm-atom { color: rgb(34, 17, 153); }
.cm-s-inner .cm-number { color: rgb(17, 102, 68); }
.cm-s-inner .cm-def { color: rgb(0, 0, 255); }
.cm-s-inner .cm-variable { color: rgb(0, 0, 0); }
.cm-s-inner .cm-variable-2 { color: rgb(0, 85, 170); }
.cm-s-inner .cm-variable-3 { color: rgb(0, 136, 85); }
.cm-s-inner .cm-string { color: rgb(170, 17, 17); }
.cm-s-inner .cm-property { color: rgb(0, 0, 0); }
.cm-s-inner .cm-operator { color: rgb(152, 26, 26); }
.cm-s-inner .cm-comment, .cm-s-inner.cm-comment { color: rgb(170, 85, 0); }
.cm-s-inner .cm-string-2 { color: rgb(255, 85, 0); }
.cm-s-inner .cm-meta { color: rgb(85, 85, 85); }
.cm-s-inner .cm-qualifier { color: rgb(85, 85, 85); }
.cm-s-inner .cm-builtin { color: rgb(51, 0, 170); }
.cm-s-inner .cm-bracket { color: rgb(153, 153, 119); }
.cm-s-inner .cm-tag { color: rgb(17, 119, 0); }
.cm-s-inner .cm-attribute { color: rgb(0, 0, 204); }
.cm-s-inner .cm-header, .cm-s-inner.cm-header { color: rgb(0, 0, 255); }
.cm-s-inner .cm-quote, .cm-s-inner.cm-quote { color: rgb(0, 153, 0); }
.cm-s-inner .cm-hr, .cm-s-inner.cm-hr { color: rgb(153, 153, 153); }
.cm-s-inner .cm-link, .cm-s-inner.cm-link { color: rgb(0, 0, 204); }
.cm-negative { color: rgb(221, 68, 68); }
.cm-positive { color: rgb(34, 153, 34); }
.cm-header, .cm-strong { font-weight: 700; }
.cm-del { text-decoration: line-through; }
.cm-em { font-style: italic; }
.cm-link { text-decoration: underline; }
.cm-error { color: red; }
.cm-invalidchar { color: red; }
.cm-constant { color: rgb(38, 139, 210); }
.cm-defined { color: rgb(181, 137, 0); }
div.CodeMirror span.CodeMirror-matchingbracket { color: rgb(0, 255, 0); }
div.CodeMirror span.CodeMirror-nonmatchingbracket { color: rgb(255, 34, 34); }
.cm-s-inner .CodeMirror-activeline-background { background-image: inherit; background-size: inherit; background-attachment: inherit; background-origin: inherit; background-clip: inherit; background-color: inherit; background-position: inherit inherit; background-repeat: inherit inherit; }
.CodeMirror { position: relative; overflow: hidden; }
.CodeMirror-scroll { height: 100%; outline: 0px; position: relative; box-sizing: content-box; background-image: inherit; background-size: inherit; background-attachment: inherit; background-origin: inherit; background-clip: inherit; background-color: inherit; background-position: inherit inherit; background-repeat: inherit inherit; }
.CodeMirror-sizer { position: relative; }
.CodeMirror-gutter-filler, .CodeMirror-hscrollbar, .CodeMirror-scrollbar-filler, .CodeMirror-vscrollbar { position: absolute; z-index: 6; display: none; }
.CodeMirror-vscrollbar { right: 0px; top: 0px; overflow: hidden; }
.CodeMirror-hscrollbar { bottom: 0px; left: 0px; overflow: hidden; }
.CodeMirror-scrollbar-filler { right: 0px; bottom: 0px; }
.CodeMirror-gutter-filler { left: 0px; bottom: 0px; }
.CodeMirror-gutters { position: absolute; left: 0px; top: 0px; padding-bottom: 30px; z-index: 3; }
.CodeMirror-gutter { white-space: normal; height: 100%; box-sizing: content-box; padding-bottom: 30px; margin-bottom: -32px; display: inline-block; }
.CodeMirror-gutter-wrapper { position: absolute; z-index: 4; border: none !important; background-position: 0px 0px !important; background-repeat: initial initial !important; }
.CodeMirror-gutter-background { position: absolute; top: 0px; bottom: 0px; z-index: 4; }
.CodeMirror-gutter-elt { position: absolute; cursor: default; z-index: 4; }
.CodeMirror-lines { cursor: text; }
.CodeMirror pre { border-top-left-radius: 0px; border-top-right-radius: 0px; border-bottom-right-radius: 0px; border-bottom-left-radius: 0px; border-width: 0px; font-family: inherit; font-size: inherit; margin: 0px; white-space: pre; word-wrap: normal; color: inherit; z-index: 2; position: relative; overflow: visible; background-position: 0px 0px; background-repeat: initial initial; }
.CodeMirror-wrap pre { word-wrap: break-word; white-space: pre-wrap; word-break: normal; }
.CodeMirror-code pre { border-right-width: 30px; border-right-style: solid; border-right-color: transparent; width: fit-content; }
.CodeMirror-wrap .CodeMirror-code pre { border-right-style: none; width: auto; }
.CodeMirror-linebackground { position: absolute; left: 0px; right: 0px; top: 0px; bottom: 0px; z-index: 0; }
.CodeMirror-linewidget { position: relative; z-index: 2; overflow: auto; }
.CodeMirror-wrap .CodeMirror-scroll { overflow-x: hidden; }
.CodeMirror-measure { position: absolute; width: 100%; height: 0px; overflow: hidden; visibility: hidden; }
.CodeMirror-measure pre { position: static; }
.CodeMirror div.CodeMirror-cursor { position: absolute; visibility: hidden; border-right-style: none; width: 0px; }
.CodeMirror div.CodeMirror-cursor { visibility: hidden; }
.CodeMirror-focused div.CodeMirror-cursor { visibility: inherit; }
.cm-searching { background-color: rgba(255, 255, 0, 0.4); background-position: initial initial; background-repeat: initial initial; }
@media print { 
  .CodeMirror div.CodeMirror-cursor { visibility: hidden; }
}


:root {
    --side-bar-bg-color: #fafafa;
    --control-text-color: #777;
}

@include-when-export url(https://fonts.loli.net/css?family=Open+Sans:400italic,700italic,700,400&subset=latin,latin-ext);

html {
    font-size: 16px;
}

body {
    font-family: "Open Sans","Clear Sans","Helvetica Neue",Helvetica,Arial,sans-serif;
    color: rgb(51, 51, 51);
    line-height: 1.6;
}

#write {
    max-width: 860px;
  	margin: 0 auto;
  	padding: 30px;
    padding-bottom: 100px;
}
#write > ul:first-child,
#write > ol:first-child{
    margin-top: 30px;
}

a {
    color: #4183C4;
}
h1,
h2,
h3,
h4,
h5,
h6 {
    position: relative;
    margin-top: 1rem;
    margin-bottom: 1rem;
    font-weight: bold;
    line-height: 1.4;
    cursor: text;
}
h1:hover a.anchor,
h2:hover a.anchor,
h3:hover a.anchor,
h4:hover a.anchor,
h5:hover a.anchor,
h6:hover a.anchor {
    text-decoration: none;
}
h1 tt,
h1 code {
    font-size: inherit;
}
h2 tt,
h2 code {
    font-size: inherit;
}
h3 tt,
h3 code {
    font-size: inherit;
}
h4 tt,
h4 code {
    font-size: inherit;
}
h5 tt,
h5 code {
    font-size: inherit;
}
h6 tt,
h6 code {
    font-size: inherit;
}
h1 {
    padding-bottom: .3em;
    font-size: 2.25em;
    line-height: 1.2;
    border-bottom: 1px solid #eee;
}
h2 {
   padding-bottom: .3em;
    font-size: 1.75em;
    line-height: 1.225;
    border-bottom: 1px solid #eee;
}
h3 {
    font-size: 1.5em;
    line-height: 1.43;
}
h4 {
    font-size: 1.25em;
}
h5 {
    font-size: 1em;
}
h6 {
   font-size: 1em;
    color: #777;
}
p,
blockquote,
ul,
ol,
dl,
table{
    margin: 0.8em 0;
}
li>ol,
li>ul {
    margin: 0 0;
}
hr {
    height: 2px;
    padding: 0;
    margin: 16px 0;
    background-color: #e7e7e7;
    border: 0 none;
    overflow: hidden;
    box-sizing: content-box;
}

li p.first {
    display: inline-block;
}
ul,
ol {
    padding-left: 30px;
}
ul:first-child,
ol:first-child {
    margin-top: 0;
}
ul:last-child,
ol:last-child {
    margin-bottom: 0;
}
blockquote {
    border-left: 4px solid #dfe2e5;
    padding: 0 15px;
    color: #777777;
}
blockquote blockquote {
    padding-right: 0;
}
table {
    padding: 0;
    word-break: initial;
}
table tr {
    border-top: 1px solid #dfe2e5;
    margin: 0;
    padding: 0;
}
table tr:nth-child(2n),
thead {
    background-color: #f8f8f8;
}
table tr th {
    font-weight: bold;
    border: 1px solid #dfe2e5;
    border-bottom: 0;
    text-align: left;
    margin: 0;
    padding: 6px 13px;
}
table tr td {
    border: 1px solid #dfe2e5;
    text-align: left;
    margin: 0;
    padding: 6px 13px;
}
table tr th:first-child,
table tr td:first-child {
    margin-top: 0;
}
table tr th:last-child,
table tr td:last-child {
    margin-bottom: 0;
}

.CodeMirror-lines {
    padding-left: 4px;
}

.code-tooltip {
    box-shadow: 0 1px 1px 0 rgba(0,28,36,.3);
    border-top: 1px solid #eef2f2;
}

.md-fences,
code,
tt {
    border: 1px solid #e7eaed;
    background-color: #f8f8f8;
    border-radius: 3px;
    padding: 0;
    padding: 2px 4px 0px 4px;
    font-size: 0.9em;
}

code {
    background-color: #f3f4f4;
    padding: 0 2px 0 2px;
}

.md-fences {
    margin-bottom: 15px;
    margin-top: 15px;
    padding-top: 8px;
    padding-bottom: 6px;
}


.md-task-list-item > input {
  margin-left: -1.3em;
}

@media print {
    html {
        font-size: 13px;
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<div  id='write'  class = 'is-mac'><h1><a name='header-n0' class='md-header-anchor '></a>gopAga2.0 Annotation</h1><hr /><h6><a name='header-n3' class='md-header-anchor '></a>#################</h6><h2><a name='header-n4' class='md-header-anchor '></a>PHASE 1</h2><p><u><strong>Run round 1 of MAKER (MAPPING EVIDENCE)</strong>—running w/30 cores on private server</u></p><p>used <em>tail -f</em> to check file progress and <em>grep -c “FIN”</em> to benchmark # of finished scaffolds. Wanted to archive opts files for each round so they were unambiguously labeled (w/ round #) and fed directly to MAKER</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; mpiexec <span class="cm-attribute">-n</span> <span class="cm-number">30</span> tools/maker/bin/maker <span class="cm-attribute">-base</span> GopAga2_rnd1 rnd1-maker_opts.ctl maker_bopts.ctl maker_exe.ctl maker_evm.ctl &amp;&gt; Gopaga2_28Dec2018.txt &amp;<span class="cm-quote">`</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 66px;"></div><div class="CodeMirror-gutters" style="display: none; height: 66px;"></div></div></div></pre><blockquote><p><strong>Start_time: 1546033072</strong></p><p><strong>End_time:   1546541976</strong></p><p><strong>Elapsed:    508904</strong></p><p><strong>Maker is now finished!!!</strong></p></blockquote><p>&nbsp;</p><p><strong>merge into single gff w/ sequences</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/bin/gff3_merge <span class="cm-attribute">-s</span> <span class="cm-attribute">-d</span> GopAga2_rnd1_master_datastore_index.log &gt; GopAga2_rnd1.all.maker.gff &amp;</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 66px;"></div><div class="CodeMirror-gutters" style="display: none; height: 66px;"></div></div></div></pre><p>&nbsp;</p><p><strong>merge into single gff <em>without</em> fasta sequence at end</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/bin/gff3_merge <span class="cm-attribute">-n</span> <span class="cm-attribute">-s</span> <span class="cm-attribute">-d</span> GopAga2_rnd1_master_datastore_index.log &gt; GopAga2_rnd1.all.maker.noseq.gff &amp;</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 66px;"></div><div class="CodeMirror-gutters" style="display: none; height: 66px;"></div></div></div></pre><p>&nbsp;</p><p><strong>merge fasta files to make <em>.maker.proteins.fasta</em> and <em>.maker.transcripts.fasta</em></strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/bin/fasta_merge <span class="cm-attribute">-d</span> GopAga2_rnd1_master_datastore_index.log  &amp;</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 44px;"></div><div class="CodeMirror-gutters" style="display: none; height: 44px;"></div></div></div></pre><p>&nbsp;</p><p><em>ROUND1 initial results</em></p><p><strong>get gene number and average length</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-builtin">cat</span> GopAga2_rnd1.all.maker.gff | <span class="cm-builtin">awk</span> <span class="cm-string">'{ if ($3 == "gene") print $0 }'</span> | <span class="cm-builtin">awk</span> <span class="cm-string">'{ sum += ($5 - $4) } END { print NR, sum / NR }’</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 44px;"></div><div class="CodeMirror-gutters" style="display: none; height: 44px;"></div></div></div></pre><blockquote><p>27255 <span>	</span>11030.7</p></blockquote><p>(#genes) (ave. length)</p><p>&nbsp;</p><p><strong>testing completion w/BUSCO</strong></p><p>run BUSCO w/ tetrapod conserved genes on transcripts called from MAKER round 1</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; ./run_BUSCO.py <span class="cm-attribute">-i</span> ../../GopAga2_rnd1.all.maker.transcripts.fasta <span class="cm-attribute">-o</span> eval_rnd1 <span class="cm-attribute">-l</span> ../tetrapoda_odb9 <span class="cm-attribute">-m</span> transcriptome <span class="cm-attribute">-c</span> <span class="cm-number">4</span> <span class="cm-attribute">-f</span> &gt; 3Jan2019_GopAga2_rnd1.out &amp;</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 88px;"></div><div class="CodeMirror-gutters" style="display: none; height: 88px;"></div></div></div></pre><blockquote><p>INFO    Results:</p><p><strong>INFO    C:67.9%[S:66.6%,D:1.3%],F:20.4%,M:11.7%,n:3950</strong></p><p>INFO    2683 Complete BUSCOs (C)</p><p>INFO    2632 Complete and single-copy BUSCOs (S)</p><p>INFO    51 Complete and duplicated BUSCOs (D)</p><p>INFO    806 Fragmented BUSCOs (F)</p><p>INFO    461 Missing BUSCOs (M)</p><p>INFO    3950 Total BUSCO groups searched</p></blockquote><p>&nbsp;</p><p><em>###TRAIN _AB INITIO</em> GENE MODELS</p><p><strong>pull confident gene models, rename</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><span><span>​</span>x</span></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/bin/maker2zff <span class="cm-attribute">-x</span> <span class="cm-number">0</span>.25 <span class="cm-attribute">-l</span> <span class="cm-number">50</span> <span class="cm-attribute">-d</span> ../GopAga2_rnd1_master_datastore_index.log</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; rename <span class="cm-string">'s/genome/GopAga2_rnd1.zff.length50_aed0.25/g’ *</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 88px;"></div><div class="CodeMirror-gutters" style="display: none; height: 88px;"></div></div></div></pre><p>&nbsp;</p><p><strong>collect gene stats, validate gene stats</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; fathom GopAga2_rnd1.zff.length50_aed0.25.ann GopAga2_rnd1.zff.length50_aed0.25.dna <span class="cm-attribute">-gene-stats</span> &gt; GopAga2_rnd1_gene-stats.log <span class="cm-number">2</span>&gt;&amp;1</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; fathom GopAga2_rnd1.zff.length50_aed0.25.ann GopAga2_rnd1.zff.length50_aed0.25.dna <span class="cm-attribute">-validate</span> &gt; GopAga2_rnd1_validate.log <span class="cm-number">2</span>&gt;&amp;1</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 154px;"></div><div class="CodeMirror-gutters" style="display: none; height: 154px;"></div></div></div></pre><p><strong>check for model errors</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-builtin">grep</span> <span class="cm-string">"error"</span> GopAga2_rnd1_validate.log</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 22px;"></div><div class="CodeMirror-gutters" style="display: none; height: 22px;"></div></div></div></pre><blockquote><p>ScCC6lQ_12_HRSCAF_137: MODEL10082 30273201 30280821 7 + errors(1): cds:internal_stop warnings(3): split-start exon-1:short(1) intron-2:GC..AG</p><p>ScCC6lQ_160086_HRSCAF_190738: MODEL10355 1905713 1916275 8 + errors(1): cds:internal_stop warnings(1): exon-8:short(5)</p><p>ScCC6lQ_161315_HRSCAF_192849: MODEL21476 5416456 5423708 5 - errors(1): cds:internal_stop warnings(1): exon-5:short(5)</p><p>ScCC6lQ_161369_HRSCAF_192903: MODEL15485 943402 944824 3 + errors(1): cds:internal_stop warnings(2): split-start exon-1:short(1)</p><p>ScCC6lQ_16796_HRSCAF_38896: MODEL25954 52568108 52572075 2 + errors(1): cds:internal_stop warnings(2): split-start exon-1:short(1)</p><p>ScCC6lQ_36_HRSCAF_515: MODEL350 95681 101320 6 + errors(1): cds:internal_stop warnings(2): split-start exon-1:short(1)</p><p>ScCC6lQ_47085_HRSCAF_74369: MODEL10491 1594991 1616418 6 - errors(1): cds:internal_stop warnings(1): exon-6:short(5)</p><p>ScCC6lQ_7897_HRSCAF_26238: MODEL10131 3388043 3423569 14 + errors(1): cds:internal_stop warnings(2): cds:incomplete exon-14:short(5)</p><p>ScCC6lQ_7897_HRSCAF_26238: MODEL10316 23414711 23417992 2 + errors(1): cds:internal_stop warnings(2): split-start exon-1:short(1)</p><p><strong>14850 genes, 14841 OK, 6770 warnings, 9 errors</strong></p></blockquote><p>&nbsp;</p><p><strong>remove erroneous gene models</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-builtin">grep</span> <span class="cm-attribute">-v</span> <span class="cm-string">'MODEL10082\|MODEL10355\|MODEL21476\|MODEL15485\|MODEL25954\|MODEL350\|MODEL10491\|MODEL10131\|MODEL10316'</span> GopAga2_rnd1.zff.length50_aed0.25.ann &gt; GopAga2_rnd1.zff.length50_aed0.25_clean.ann</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 110px;"></div><div class="CodeMirror-gutters" style="display: none; height: 110px;"></div></div></div></pre><p>&nbsp;</p><p><strong>re-validate models &amp; grep for errors</strong> </p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt;fathom GopAga2_rnd1.zff.length50_aed0.25_clean.ann GopAga2_rnd1.zff.length50_aed0.25.dna <span class="cm-attribute">-validate</span> &gt; GopAga2_rnd1_validate_clean.log <span class="cm-number">2</span>&gt;&amp;1</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt;grep <span class="cm-string">"error"</span> GopAga2_rnd1_validate_clean.log</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 110px;"></div><div class="CodeMirror-gutters" style="display: none; height: 110px;"></div></div></div></pre><blockquote><p><strong><em>14834 genes, 14834 OK, 6759 warnings, 0 errors</em></strong></p><p>&nbsp;</p></blockquote><p>&nbsp;</p><p><strong>break into types of genes and gather 1000 bp on either side (generates several files)</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; fathom GopAga2_rnd1.zff.length50_aed0.25_clean.ann GopAga2_rnd1.zff.length50_aed0.25.dna <span class="cm-attribute">-categorize</span> <span class="cm-number">1000</span> &gt; GopAga2_rnd1_categorize.log <span class="cm-number">2</span>&gt;&amp;1 &amp;</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 66px;"></div><div class="CodeMirror-gutters" style="display: none; height: 66px;"></div></div></div></pre><blockquote><p>alt.ann, alt.dna (genes with alternative splicing)</p><p>err.ann, err.dna (genes that have errors)</p><p>olp.ann, olp.dna (genes that overlap other genes)</p><p>wrn.ann, wrn.dna (genes with warnings)</p><p>uni.ann, uni.dna (single gene per sequence)</p></blockquote><p>&nbsp;</p><p><strong>convert to plus strand</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; fathom uni.ann uni.dna <span class="cm-attribute">-export</span> <span class="cm-number">1000</span> <span class="cm-attribute">-plus</span> &gt; uni-plus.log <span class="cm-number">2</span>&gt;&amp;1</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 22px;"></div><div class="CodeMirror-gutters" style="display: none; height: 22px;"></div></div></div></pre><p>&nbsp;</p><p><strong>params &amp; generate hmm</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-builtin">mkdir</span> params</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-builtin">cd</span> params/</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; forge ../export.ann ../export.dna &gt; ../forge.log <span class="cm-number">2</span>&gt;&amp;1</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-builtin">cd</span> ..</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; hmm-assembler.pl GopAga2_rnd1.zff.length50_aed0.25 params &gt; GopAga2_rnd1.zff.length50_aed0.25.hmm</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 132px;"></div><div class="CodeMirror-gutters" style="display: none; height: 132px;"></div></div></div></pre><p>&nbsp;</p><p><strong><em>ready to run next phase, but first need to modify MAKER control file (opts.ctl) for round 2</em></strong></p><p><em>changed opts file to remove all est, protein, repeat info, changed est2genome and protein2genome to 0, added the .gff files for est, protein, repeats.</em> Will run much faster without mapping evidence and instead being passed gffs produced from the first round.</p><hr /><h2><a name='header-n90' class='md-header-anchor '></a>PHASE 2</h2><p><u><strong>Run round 2 of MAKER (first <em>ab initio</em> run (i.e. SNAP round1))</strong></u></p><p><strong>run maker</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; mpiexec <span class="cm-attribute">-n</span> <span class="cm-number">30</span> tools/maker/bin/maker <span class="cm-attribute">-base</span> GopAga2_rnd2 rnd2-maker_opts.ctl maker_bopts.ctl maker_exe.ctl maker_evm.ctl &amp;&gt; Gopaga2_3Jan2019.txt &amp;</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 66px;"></div><div class="CodeMirror-gutters" style="display: none; height: 66px;"></div></div></div></pre><p><em>finished in &lt;12 hrs</em></p><p>&nbsp;</p><p><strong>merege single gff w/ sequences, merge fastas, merge single gff w/out sequences</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/bin/gff3_merge <span class="cm-attribute">-s</span> <span class="cm-attribute">-d</span> GopAga2_rnd2_master_datastore_index.log &gt; GopAga2_rnd2.all.maker.gff</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/bin/fasta_merge <span class="cm-attribute">-d</span> GopAga2_rnd2_master_datastore_index.log</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/bin/gff3_merge <span class="cm-attribute">-n</span> <span class="cm-attribute">-s</span> <span class="cm-attribute">-d</span> GopAga2_rnd2_master_datastore_index.log &gt; GopAga2_rnd2.all.maker.noseq.gff</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 176px;"></div><div class="CodeMirror-gutters" style="display: none; height: 176px;"></div></div></div></pre><p>&nbsp;</p><p><em>ROUND2 results</em></p><p><strong>check AED distribution</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/exe/Genome_annotation/AED_cdf_generator.pl <span class="cm-attribute">-b</span> <span class="cm-number">0</span>.025 GopAga2_rnd2.all.maker.gff &gt; GopAga2_rnd2_AED_dist.out</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 44px;"></div><div class="CodeMirror-gutters" style="display: none; height: 44px;"></div></div></div></pre><blockquote><p><strong>AED</strong> <strong>GopAga2_rnd2.all.maker.gff</strong></p><p><strong>0.000</strong> <strong>0.073</strong></p><p><strong>0.025</strong> <strong>0.157</strong></p><p><strong>0.050</strong> <strong>0.258</strong></p><p><strong>0.075</strong> <strong>0.313</strong></p><p><strong>0.100</strong> <strong>0.383</strong></p><p><strong>0.125</strong> <strong>0.421</strong></p><p><strong>0.150</strong> <strong>0.476</strong></p><p><strong>0.175</strong> <strong>0.508</strong></p><p><strong>0.200</strong> <strong>0.551</strong></p><p><strong>0.225</strong> <strong>0.577</strong></p><p><strong>0.250</strong> <strong>0.614</strong></p><p><strong>0.275</strong> <strong>0.637</strong></p><p><strong>0.300</strong> <strong>0.669</strong></p><p><strong>0.325</strong> <strong>0.689</strong></p><p><strong>0.350</strong> <strong>0.721</strong></p><p><strong>0.375</strong> <strong>0.740</strong></p><p><strong>0.400</strong> <strong>0.768</strong></p><p><strong>0.425</strong> <strong>0.786</strong></p><p><strong>0.450</strong> <strong>0.816</strong></p><p><strong>0.475</strong> <strong>0.844</strong></p><p><strong>0.500 0.879</strong></p><p>0.525 0.887</p><p>0.550 0.898</p><p>0.575 0.905</p><p>0.600 0.914</p><p>0.625 0.919</p><p>0.650 0.928</p><p>0.675 0.933</p><p>0.700 0.940</p><p>0.725 0.945</p><p>0.750 0.951</p><p>0.775 0.955</p><p>0.800 0.962</p><p>0.825 0.966</p><p>0.850 0.973</p><p>0.875 0.977</p><p>0.900 0.983</p><p>0.925 0.987</p><p>0.950 0.993</p><p>0.975 0.997</p><p>1.000 1.000</p></blockquote><p>~88% of models have an AED of 0.5 or under (goal is 95% according to <strong>CITATION</strong>)</p><p>&nbsp;</p><p><strong>get # genes and average lengths</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-builtin">cat</span> GopAga2_rnd2.all.maker.gff | <span class="cm-builtin">awk</span> <span class="cm-string">'{ if ($3 == "gene") print $0 }'</span> | <span class="cm-builtin">awk</span> <span class="cm-string">'{ sum += ($5 - $4) } END { print NR, sum / NR }'</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 44px;"></div><div class="CodeMirror-gutters" style="display: none; height: 44px;"></div></div></div></pre><blockquote><p><strong>24984 29839.9</strong></p></blockquote><p>&nbsp;</p><p><strong>check BUSCO completeness</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">./run_BUSCO.py <span class="cm-attribute">-i</span> ../GopAga2_Jan2018/GopAga2_rnd2.all.maker.transcripts.fasta <span class="cm-attribute">-o</span> eval_rnd2 <span class="cm-attribute">-l</span> ../tetrapoda_odb9 <span class="cm-attribute">-m</span> transcriptome <span class="cm-attribute">-c</span> <span class="cm-number">4</span> &gt; 4Jan2019_GopAga2_rnd2.out &amp;</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 88px;"></div><div class="CodeMirror-gutters" style="display: none; height: 88px;"></div></div></div></pre><blockquote><p><strong>C:71.9%[S:70.9%,D:1.0%],F:17.6%,M:10.5%,n:3950</strong></p><p>        2841    Complete BUSCOs (C)</p><p>        2802    Complete and single-copy BUSCOs (S)</p><p>        39      Complete and duplicated BUSCOs (D)</p><p>        697     Fragmented BUSCOs (F)</p><p>        412     Missing BUSCOs (M)</p><p>        3950    Total BUSCO groups searched</p></blockquote><p>some improvement—1.2% fewer missing BUSCOs</p><p>&nbsp;</p><p><strong><em>TRAINING SNAP2-------------</em></strong></p><p>&nbsp;</p><p><strong>pull confident gene models, rename, collect gene stats, validate genes, check for erroneous models</strong> </p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/bin/maker2zff <span class="cm-attribute">-x</span> <span class="cm-number">0</span>.25 <span class="cm-attribute">-l</span> <span class="cm-number">50</span> <span class="cm-attribute">-d</span> ../GopAga2_rnd2_master_datastore_index.log</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; rename <span class="cm-string">'s/genome/GopAga2_rnd2.zff.length50_aed0.25/g'</span> *</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; fathom GopAga2_rnd2.zff.length50_aed0.25.ann GopAga2_rnd2.zff.length50_aed0.25.dna <span class="cm-attribute">-gene-stats</span> &gt; GopAga2_rnd2_gene-stats.log <span class="cm-number">2</span>&gt;&amp;1</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; fathom GopAga2_rnd2.zff.length50_aed0.25.ann GopAga2_rnd2.zff.length50_aed0.25.dna <span class="cm-attribute">-validate</span> &gt; GopAga2_rnd2_validate.log <span class="cm-number">2</span>&gt;&amp;1</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-builtin">grep</span> <span class="cm-string">"error"</span> GopAga2_rnd2_validate.log</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 330px;"></div><div class="CodeMirror-gutters" style="display: none; height: 330px;"></div></div></div></pre><blockquote><p>ScCC6lQ_161315_HRSCAF_192849: MODEL19261 5416456 5423708 5 - errors(1): cds:internal_stop warnings(1): exon-5:short(5)</p><p>ScCC6lQ_47085_HRSCAF_74369: MODEL8635 1594991 1616552 8 - errors(1): cds:internal_stop warnings(1): exon-8:short(5)</p><p><strong>10462 genes, 10460 OK, 2860 warnings, 2 errors</strong></p></blockquote><p>&nbsp;</p><p><strong>remove erroneous gene models, re-validate, re-grep for errors</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-builtin">grep</span> <span class="cm-attribute">-v</span> <span class="cm-string">'MODEL19261\|MODEL8635'</span> GopAga2_rnd2.zff.length50_aed0.25.ann &gt; GopAga2_rnd2.zff.length50_aed0.25_clean.ann</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; fathom GopAga2_rnd2.zff.length50_aed0.25_clean.ann GopAga2_rnd2.zff.length50_aed0.25.dna <span class="cm-attribute">-validate</span> GopAga2_rnd2_validate_clean.log <span class="cm-number">2</span>&gt;&amp;1</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt;grep <span class="cm-string">"error"</span> GopAga2_rnd2_validate_clean.log</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 198px;"></div></div></div></pre><blockquote><p><strong>10460 genes, 10460 OK, 2858 warnings, 0 errors</strong></p></blockquote><p>&nbsp;</p><p><strong>grab genes w/ 1000bp on either side, convert to plus strand, do params, generate hmm</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; fathom GopAga2_rnd2.zff.length50_aed0.25_clean.ann GopAga2_rnd2.zff.length50_aed0.25.dna <span class="cm-attribute">-categorize</span> <span class="cm-number">1000</span> &gt; GopAga2_rnd2_categorize.log <span class="cm-number">2</span>&gt;&amp;1</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; fathom uni.ann uni.dna <span class="cm-attribute">-export</span> <span class="cm-number">1000</span> <span class="cm-attribute">-plus</span> &gt; uni-plus.log <span class="cm-number">2</span>&gt;&amp;1</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-builtin">mkdir</span> params</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-builtin">cd</span> params/</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; forge ../export.ann ../export.dna &gt; ../forge.log <span class="cm-number">2</span>&gt;&amp;1</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-builtin">cd</span> ..</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; hmm-assembler.pl GopAga2_rnd2.zff.length50_aed0.25 params &gt; GopAga2_rnd2.zff.length50_aed0.25.hmm</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 352px;"></div><div class="CodeMirror-gutters" style="display: none; height: 352px;"></div></div></div></pre><p>&nbsp;</p><p><strong><em>TRAINING AUGUSTUS1-------------</em></strong></p><p><em>copied zff2augustus.pl to working folder</em> — the zff2augustus.pl script is available <strong>HERE</strong></p><p>&nbsp;</p><p><strong>make gbk file for augustus using export.ann and export.dna files from SNAP2 training</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; ./zff2augustus_gbk.pl &gt; GopAga2_augustus1.gbk</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 22px;"></div><div class="CodeMirror-gutters" style="display: none; height: 22px;"></div></div></div></pre><p><strong>split into training and dest set</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/exe/Augustus/scripts/randomSplit.pl GopAga2_augustus1.gbk <span class="cm-number">100</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 44px;"></div><div class="CodeMirror-gutters" style="display: none; height: 44px;"></div></div></div></pre><p><em>this produced <strong>GopAga2_augustus1.gbk.test</strong> and <strong>GopAga2_augustus1.gbk.train</strong> files</em></p><p>&nbsp;</p><p><strong>make a new augustus species</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-keyword">export</span> <span class="cm-def">AUGUSTUS_CONFIG_PATH</span><span class="cm-operator">=</span>tools/maker/exe/Augustus/config</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/exe/Augustus/scripts/new_species.pl <span class="cm-attribute">--species</span><span class="cm-operator">=</span>rGopaga2-0</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 88px;"></div><div class="CodeMirror-gutters" style="display: none; height: 88px;"></div></div></div></pre><blockquote><p>Will create parameters for a EUKARYOTIC species!</p><p>creating directory tools/maker/exe/Augustus/config/species/rGopaga2-0/</p><p>creating tools/maker/exe/Augustus/config/species/rGopaga2-0/rGopaga2-0_parameters.cfg </p><p>creating tools/maker/exe/Augustus/config/species/rGopaga2-0/rGopaga2-0_weightmatrix.txt</p><p>creating tools/maker/exe/Augustus/config/species/rGopaga2-0/rGopaga2-0_metapars.cfg</p><p>The necessary files for training rGopaga2-0 have been created.</p><p>Now, either run etraining or* <a href='http://optimize_parameters.pl'>optimize_parameters.pl</a> *with --species=rGopaga2-0. </p><p>etraining quickly estimates the parameters from a file with training genes.</p><p><a href='http://optimize_augustus.pl'>optimize_augustus.pl</a> alternates running etraining and augustus to find optimal metaparameters. </p></blockquote><p>&nbsp;</p><p><strong>first Augustus etraining of species rGopaga2-0</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/exe/Augustus/bin/etraining <span class="cm-attribute">--species</span><span class="cm-operator">=</span>rGopaga2-0 GopAga2_augustus1.gbk.train &gt; rGopaga2_augustus1Training1.out</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/exe/Augustus/bin/augustus <span class="cm-attribute">--species</span><span class="cm-operator">=</span>rGopaga2-0 GopAga2_augustus1.gbk.test | <span class="cm-builtin">tee</span> rGopaga2-0_firsttraining-test.out</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 132px;"></div><div class="CodeMirror-gutters" style="display: none; height: 132px;"></div></div></div></pre><blockquote><p><strong>**</strong>*      Evaluation of gene prediction     <strong>**</strong>*</p><p>---------------------------------------------\</p><p>                 | sensitivity | specificity |</p><p>---------------------------------------------|</p><p><strong>nucleotide level |       0.876 |       0.814 |</strong></p><p>---------------------------------------------/</p><p>----------------------------------------------------------------------------------------------------------\</p><p>           |  #pred |  #anno |      |    FP = false pos. |    FN = false neg. |             |             |</p><p>           | total/ | total/ |   TP |--------------------|--------------------| sensitivity | specificity |</p><p>           | unique | unique |      | part | ovlp | wrng | part | ovlp | wrng |             |             |</p><p>----------------------------------------------------------------------------------------------------------|</p><p>           |        |        |      |                223 |                229 |             |             |</p><p>exon level |    771 |    777 |  548 | ------------------ | ------------------ |       <strong>0.705 |       0.711 |</strong></p><p>           |    771 |    777 |      |  100 |    9 |  114 |  100 |    8 |  121 |             |             |</p><p>----------------------------------------------------------------------------------------------------------/</p><p>----------------------------------------------------------------------------\</p><p>transcript | #pred | #anno |   TP |   FP |   FN | sensitivity | specificity |</p><p>----------------------------------------------------------------------------|</p><p>gene level |   119 |   100 |   12 |  107 |   88 |        <strong>0.12 |       0.101 |</strong></p><p>----------------------------------------------------------------------------/</p><p>------------------------------------------------------------------------\</p><p>            UTR | total pred | CDS bnd. corr. |   meanDiff | medianDiff |</p><p>------------------------------------------------------------------------|</p><p>            TSS |         25 |              0 |         -1 |         -1 |</p><p>            TTS |          6 |              0 |         -1 |         -1 |</p><p>------------------------------------------------------------------------|</p><p>            UTR | uniq. pred |    unique anno |      sens. |      spec. |</p><p>------------------------------------------------------------------------|</p><p>                |  true positive = 1 bound. exact, 1 bound. &lt;= 20bp off |</p><p>UTR exon level |          0 |              0 |       -nan |       -nan |</p><p>------------------------------------------------------------------------|</p><p>UTR base level |          0 |              0 |       -nan |       -nan |</p><p>------------------------------------------------------------------------/</p><p>nucUTP= 0 nucUFP=0 nucUFPinside= 0 nucUFN=0</p><p># total time: 177</p></blockquote><p>First few metrics aren&#39;t bad, but gene statistics are not good—target for these when developing gene models for non-model organisms are XXXX (REF)</p><p>&nbsp;</p><p><strong>Augustus optomization of rGopaga2-0</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/exe/Augustus/scripts/optimize_augustus.pl <span class="cm-attribute">--species</span><span class="cm-operator">=</span>rGopaga2-0 GopAga2_augustus1.gbk.train <span class="cm-attribute">--cpus</span><span class="cm-operator">=</span><span class="cm-number">16</span> <span class="cm-attribute">--kfold</span><span class="cm-operator">=</span><span class="cm-number">16</span> &gt; Gopaga2-0_optomizeAug.out &amp;</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 66px;"></div><div class="CodeMirror-gutters" style="display: none; height: 66px;"></div></div></div></pre><p><strong>Augustus etraining after optomization, then re-testing</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/exe/Augustus/bin/etraining <span class="cm-attribute">--species</span><span class="cm-operator">=</span>rGopaga2-0 GopAga2_augustus1.gbk.train &gt; rGopaga2_augustus1Training2.out</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/exe/Augustus/bin/augustus <span class="cm-attribute">--species</span><span class="cm-operator">=</span>rGopaga2-0 GopAga2_augustus1.gbk.test | <span class="cm-builtin">tee</span> rGopaga2_augustus1Training2-test.out</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 132px;"></div><div class="CodeMirror-gutters" style="display: none; height: 132px;"></div></div></div></pre><blockquote><p><strong><em>*</em>*<em>*</em>      Evaluation of gene prediction     *<em>*</em>***</strong></p><p><strong>---------------------------------------------**</strong></p><p>                 <strong>| sensitivity | specificity |</strong></p><p><strong>---------------------------------------------|</strong></p><p><strong>nucleotide level |       0.914 |       0.812 |</strong></p><p><strong>---------------------------------------------/</strong></p><p><strong>----------------------------------------------------------------------------------------------------------**</strong>**</p><p>           <strong>|  #pred |  #anno |      |    FP = false pos. |    FN = false neg. |             |             |</strong></p><p>           <strong>| total/ | total/ |   TP |--------------------|--------------------| sensitivity | specificity |</strong></p><p>           <strong>| unique | unique |      | part | ovlp | wrng | part | ovlp | wrng |             |             |</strong></p><p><strong>----------------------------------------------------------------------------------------------------------|</strong></p><p>           <strong>|        |        |      |                244 |                199 |             |             |</strong></p><p><strong>exon level |    822 |    777 |  578 | ------------------ | ------------------ |       0.744 |       0.703 |</strong></p><p>           <strong>|    822 |    777 |      |  112 |    7 |  125 |  112 |    6 |   81 |             |             |</strong></p><p><strong>----------------------------------------------------------------------------------------------------------/</strong></p><p><strong>----------------------------------------------------------------------------**</strong>**</p><p><strong>transcript | #pred | #anno |   TP |   FP |   FN | sensitivity | specificity |</strong></p><p><strong>----------------------------------------------------------------------------|</strong></p><p><strong>gene level |   122 |   100 |   12 |  110 |   88 |        0.12 |      0.0984 |</strong></p><p><strong>----------------------------------------------------------------------------/</strong></p><p><strong>------------------------------------------------------------------------**</strong>**</p><p>            <strong>UTR | total pred | CDS bnd. corr. |   meanDiff | medianDiff |</strong></p><p><strong>------------------------------------------------------------------------|</strong></p><p>            <strong>TSS |         32 |              0 |         -1 |         -1 |</strong></p><p>            <strong>TTS |          4 |              0 |         -1 |         -1 |</strong></p><p><strong>------------------------------------------------------------------------|</strong></p><p>            <strong>UTR | uniq. pred |    unique anno |      sens. |      spec. |</strong></p><p><strong>------------------------------------------------------------------------|</strong></p><p>                <strong>|  true positive = 1 bound. exact, 1 bound. &lt;= 20bp off |</strong></p><p><strong>UTR exon level |          0 |              0 |       -nan |       -nan |</strong></p><p><strong>------------------------------------------------------------------------|</strong></p><p><strong>UTR base level |          0 |              0 |       -nan |       -nan |</strong></p><p><strong>------------------------------------------------------------------------/</strong></p></blockquote><p>improved sensitivity/specificity for nucleotide and exon statistics, but not for the overall gene level. The developers note that if the exons aren&#39;t called exactly correctly then the gene level will have poor statistics :/</p><p>—we&#39;ll move on and see what this does for predicting genes in the next round of MAKER</p><p><strong>edit the maker control file </strong></p><hr /><h3><a name='header-n285' class='md-header-anchor '></a> </h3><h2><a name='header-n286' class='md-header-anchor '></a>PHASE 3</h2><p><u><strong>Run round 3 of MAKER (second <em>ab initio</em> run (i.e. SNAP round2, Augustus round1))</strong></u></p><p><strong>run maker</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; mpiexec <span class="cm-attribute">-n</span> <span class="cm-number">30</span> tools/maker/bin/maker <span class="cm-attribute">-base</span> GopAga2_rnd3 rnd3-maker_opts.ctl maker_bopts.ctl &gt; maker_exe.ctl maker_evm.ctl &amp;&gt; Gopaga2_12Jan2019.txt &amp;</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 66px;"></div><div class="CodeMirror-gutters" style="display: none; height: 66px;"></div></div></div></pre><p>&nbsp;</p><p><strong>merge into gff and fastas</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/bin/gff3_merge <span class="cm-attribute">-s</span> <span class="cm-attribute">-d</span> GopAga2_rnd3_master_datastore_index.log &gt; GopAga2_rnd3.all.maker.gff</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/bin/gff3_merge <span class="cm-attribute">-n</span> <span class="cm-attribute">-s</span> <span class="cm-attribute">-d</span> GopAga2_rnd3_master_datastore_index.log &gt; GopAga2_rnd3.all.maker.noseq.gff</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text="">​</span></span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; tools/maker/bin/fasta_merge <span class="cm-attribute">-d</span> GopAga2_rnd3_master_datastore_index.log</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 220px;"></div><div class="CodeMirror-gutters" style="display: none; height: 220px;"></div></div></div></pre><p>&nbsp;</p><p><em>RESULTS FROM ROUND 3</em></p><p>&nbsp;</p><p><strong>get gene count &amp; length</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-builtin">cat</span> GopAga2_rnd3.all.maker.gff | <span class="cm-builtin">awk</span> <span class="cm-string">'{ if ($3 == "gene") print $0 }'</span> | <span class="cm-builtin">awk</span> <span class="cm-string">'{ sum += ($5 - $4) } END { print NR, sum / NR }'</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 44px;"></div><div class="CodeMirror-gutters" style="display: none; height: 44px;"></div></div></div></pre><blockquote><p><strong><em>25338 21155.2</em></strong></p></blockquote><p>&nbsp;</p><p><strong>get AED distribution</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">@@@@@@@@@@@@@@@@@@@@@@@@</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 22px;"></div><div class="CodeMirror-gutters" style="display: none; height: 22px;"></div></div></div></pre><blockquote><p><strong>AED     GopAga2_rnd3.all.maker.gff</strong></p><p><strong>0.000   0.094</strong></p><p><strong>0.025   0.200</strong></p><p><strong>0.050   0.325</strong></p><p><strong>0.075   0.391</strong></p><p><strong>0.100   0.470</strong></p><p><strong>0.125   0.514</strong></p><p><strong>0.150   0.574</strong></p><p><strong>0.175   0.608</strong></p><p><strong>0.200   0.652</strong></p><p><strong>0.225   0.678</strong></p><p><strong>0.250   0.712</strong></p><p><strong>0.275   0.733</strong></p><p><strong>0.300   0.762</strong></p><p><strong>0.325   0.778</strong></p><p><strong>0.350   0.801</strong></p><p><strong>0.375   0.815</strong></p><p><strong>0.400   0.833</strong></p><p><strong>0.425   0.845</strong></p><p><strong>0.450   0.867</strong></p><p><strong>0.475   0.888</strong></p><p><strong>0.500   0.913</strong></p><p>0.525   0.918</p><p>0.550   0.925</p><p>0.575   0.929</p><p>0.600   0.935</p><p>0.625   0.938</p><p>0.650   0.944</p><p>0.675   0.948</p><p>0.700   0.953</p><p>0.725   0.956</p><p>0.750   0.960</p><p>0.775   0.964</p><p>0.800   0.968</p><p>0.825   0.972</p><p>0.850   0.977</p><p>0.875   0.980</p><p>0.900   0.985</p><p>0.925   0.988</p><p>0.950   0.994</p><p>0.975   0.997</p><p>1.000   1.000</p></blockquote><p>this is an improvement of 3-4%, current is 91.3%, goal is 95%</p><p>&nbsp;</p><p><strong>BUSCO</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">@@@@@@@@@@@@@@@@@@@@@@@@</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 22px;"></div><div class="CodeMirror-gutters" style="display: none; height: 22px;"></div></div></div></pre><blockquote><p>INFO    Results:</p><p><strong>INFO    C:75.7%[S:74.6%,D:1.1%],F:16.4%,M:7.9%,n:3950</strong></p><p>INFO    2990 Complete BUSCOs (C)</p><p>INFO    2945 Complete and single-copy BUSCOs (S)</p><p>INFO    45 Complete and duplicated BUSCOs (D)</p><p>INFO    648 Fragmented BUSCOs (F)</p><p>INFO    312 Missing BUSCOs (M)</p><p>INFO    3950 Total BUSCO groups searched</p><p>INFO    BUSCO analysis done. Total running time: 3663.44585299 seconds</p></blockquote><p>This is an improvement, gopAga1.0 had 8.5% missing BUSCOs and MAKER round2 for gopAga2.0 had 10.5, so this is looking better</p><p>&nbsp;</p><p><strong><em>TRAINING SNAP3-------------</em></strong></p><p>&nbsp;</p><p><strong>pull confident gene models, rename, collect gene stats, validate genes, check for erroneous models</strong> </p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n365" mdtype="fences">&gt; tools/maker/bin/maker2zff -x 0.25 -l 50 -d ../GopAga2_rnd3_master_datastore_index.log

&gt; rename 's/genome/GopAga2_rnd3.zff.length50_aed0.25/g' *

&gt; fathom GopAga2_rnd3.zff.length50_aed0.25.ann GopAga2_rnd3.zff.length50_aed0.25.dna -gene-stats &gt; GopAga2_rnd3_gene-stats.log 2&gt;&amp;1

&gt; fathom GopAga2_rnd3.zff.length50_aed0.25.ann GopAga2_rnd3.zff.length50_aed0.25.dna -validate &gt; GopAga2_rnd3_validate.log 2&gt;&amp;1

&gt; grep "error" GopAga2_rnd3_validate.log
</pre><blockquote><p>ScCC6lQ_159743_HRSCAF_190215: MODEL7484 278734 279715 2 + errors(1): cds:internal_stop warnings(2): split-start exon-1:short(1)</p><p>ScCC6lQ_3500_HRSCAF_17357: MODEL6547 391007 402577 5 - errors(1): cds:internal_stop warnings(2): exon-5:short(5) intron-4:GA..AG</p><p>ScCC6lQ_47085_HRSCAF_74369: MODEL9960 1594991 1616418 7 - errors(1): cds:internal_stop warnings(1): exon-7:short(5)</p><p><strong>12115 genes, 12112 OK, 2684 warnings, 3 errors</strong></p></blockquote><p>&nbsp;</p><p><strong>remove erroneous gene models, re-validate, re-grep for errors</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n373" mdtype="fences">&gt; grep -v 'MODEL7484\|MODEL6547\|MODEL9960' GopAga2_rnd3.zff.length50_aed0.25.ann &gt; GopAga2_rnd3.zff.length50_aed0.25_clean.ann

&gt; fathom GopAga2_rnd3.zff.length50_aed0.25_clean.ann GopAga2_rnd3.zff.length50_aed0.25.dna -validate &gt; GopAga2_rnd3_validate_clean.log

&gt; grep "error" GopAga2_rnd3_validate_clean.log
</pre><blockquote><p>no errors</p></blockquote><p>&nbsp;</p><p><strong>grab genes w/ 1000bp on either side, convert to plus strand, do params, generate hmm</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n378" mdtype="fences">&gt; fathom GopAga2_rnd3.zff.length50_aed0.25_clean.ann GopAga2_rnd3.zff.length50_aed0.25.dna -categorize 1000 &gt; GopAga2_rnd3_categorize.log 2&gt;&amp;1

&gt; fathom uni.ann uni.dna -export 1000 -plus &gt; uni-plus.log 2&gt;&amp;1

&gt; mkdir params

&gt; cd params/

&gt; forge ../export.ann ../export.dna &gt; ../forge.log 2&gt;&amp;1

&gt; hmm-assembler.pl GopAga2_rnd3.zff.length50_aed0.25 params &gt; GopAga2_rnd3.zff.length50_aed0.25.hmm
</pre><p>&nbsp;</p><p><strong><em>TRAINING AUGUSTUS2-------------</em></strong></p><p><em>copied zff2augustus.pl to working folder</em> — the zff2augustus.pl script is available <strong>HERE</strong></p><p>&nbsp;</p><p><strong>make gbk file for augustus using export.ann and export.dna files from SNAP2 training</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="" contenteditable="false" cid="n384" mdtype="fences">&gt; ./zff2augustus_gbk.pl &gt; GopAga2_augustus2.gbk
</pre><p>&nbsp;</p><p><strong>split into training and test sets</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="" contenteditable="false" cid="n387" mdtype="fences">&gt; tools/maker/exe/Augustus/scripts/randomSplit.pl GopAga2_augustus2.gbk 100
</pre><p><strong>etraining of species rGopaga2-0 (first etraining of Augustus round2)</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="" contenteditable="false" cid="n389" mdtype="fences">&gt; tools/maker/exe/Augustus/bin/etraining --species=rGopaga2-0 GopAga2_augustus2.gbk.train &gt; rGopaga2_augustus2Training1.out
</pre><p>&nbsp;</p><p><strong>testing rGopaga2-0 species</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n392" mdtype="fences">&gt; tools/maker/exe/Augustus/bin/augustus --species=rGopaga2-0 GopAga2_augustus2.gbk.test | tee rGopaga2_augustus2firstTraining-test.out
</pre><blockquote><p>a-posteriori probability of viterbi path</p><p>----------------------------------------</p><p>a-posteriori probability of correct path</p><p>100 times were the paths equally likely (identical).</p><p>sorted quotients of the rest:</p><p>0 quotients were between 1 and 10</p><p><strong>**</strong>*      Evaluation of gene prediction     <strong>**</strong>*</p><p>---------------------------------------------\</p><p>                 | sensitivity | specificity |</p><p>---------------------------------------------|</p><p><strong>nucleotide level |       0.914 |         0.8 |</strong></p><p>---------------------------------------------/</p><p>----------------------------------------------------------------------------------------------------------\</p><p>           |  #pred |  #anno |      |    FP = false pos. |    FN = false neg. |             |             |</p><p>           | total/ | total/ |   TP |--------------------|--------------------| sensitivity | specificity |</p><p>           | unique | unique |      | part | ovlp | wrng | part | ovlp | wrng |             |             |</p><p>----------------------------------------------------------------------------------------------------------|</p><p>           |        |        |      |                275 |                232 |             |             |</p><p>exon level |   1085 |   1042 |  810 | ------------------ | ------------------ |       <strong>0.777 |       0.747 |</strong></p><p>           |   1085 |   1042 |      |  113 |    3 |  159 |  113 |    3 |  116 |             |             |</p><p>----------------------------------------------------------------------------------------------------------/</p><p>----------------------------------------------------------------------------\</p><p>transcript | #pred | #anno |   TP |   FP |   FN | sensitivity | specificity |</p><p>----------------------------------------------------------------------------|</p><p>gene level |   141 |   100 |   17 |  124 |   83 |        <strong>0.17 |       0.121 |</strong></p><p>----------------------------------------------------------------------------/</p><p>------------------------------------------------------------------------\</p><p>            UTR | total pred | CDS bnd. corr. |   meanDiff | medianDiff |</p><p>------------------------------------------------------------------------|</p><p>            TSS |         22 |              0 |         -1 |         -1 |</p><p>            TTS |          5 |              0 |         -1 |         -1 |</p><p>------------------------------------------------------------------------|</p><p>            UTR | uniq. pred |    unique anno |      sens. |      spec. |</p><p>------------------------------------------------------------------------|</p><p>                |  true positive = 1 bound. exact, 1 bound. &lt;= 20bp off |</p><p>UTR exon level |          0 |              0 |       -nan |       -nan |</p><p>------------------------------------------------------------------------|</p><p>UTR base level |          0 |              0 |       -nan |       -nan |</p><p>------------------------------------------------------------------------/</p></blockquote><p>gene level statistics improved quite a lot. still not quite reaching our goal.</p><p>&nbsp;</p><p><strong>testing rGopaga2-0 species</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n436" mdtype="fences">&gt; Augustus/scripts/optimize_augustus.pl --species=rGopaga2-0 GopAga2_augustus2.gbk.train --cpus=8 --kfold=8 &gt; Gopaga2-0_optomizeAug_v2May2019.out &amp;
</pre><p><em>note—this seems to take a while (~a week for this round using 8 cores). The kfold number has to equal the cpu number, so it’s not clear whether increasing these gives a clear speed payoff</em></p><p>&nbsp;</p><p><strong>etraining after optomization</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n440" mdtype="fences">&gt; tools/maker/exe/Augustus/bin/etraining --species=rGopaga2-0 GopAga2_augustus2.gbk.train &gt; rGopaga2_augustus2Training2.out
</pre><p>&nbsp;</p><p><strong>testing Augustus species after optomization &amp; etraining</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n443" mdtype="fences">maker/exe/Augustus/bin/augustus --species=rGopaga2-0 GopAga2_augustus2.gbk.test | tee rGopaga2_augustus2secondTraining-test.out
</pre><p>&nbsp;</p><blockquote><p><strong>**</strong>*      Evaluation of gene prediction     <strong>**</strong>*</p><p>---------------------------------------------\</p><p>                 | sensitivity | specificity |</p><p>---------------------------------------------|</p><p>nucleotide level |       <strong>0.914 |       0.802 |</strong></p><p>---------------------------------------------/</p><p>----------------------------------------------------------------------------------------------------------\</p><p>           |  #pred |  #anno |      |    FP = false pos. |    FN = false neg. |             |             |</p><p>           | total/ | total/ |   TP |--------------------|--------------------| sensitivity | specificity |</p><p>           | unique | unique |      | part | ovlp | wrng | part | ovlp | wrng |             |             |</p><p>----------------------------------------------------------------------------------------------------------|</p><p>           |        |        |      |                272 |                233 |             |             |</p><p>exon level |   1081 |   1042 |  809 | ------------------ | ------------------ |       <strong>0.776 |       0.748 |</strong></p><p>           |   1081 |   1042 |      |  113 |    3 |  156 |  114 |    3 |  116 |             |             |</p><p>----------------------------------------------------------------------------------------------------------/</p><p>----------------------------------------------------------------------------\</p><p>transcript | #pred | #anno |   TP |   FP |   FN | sensitivity | specificity |</p><p>----------------------------------------------------------------------------|</p><p>gene level |   140 |   100 |   17 |  123 |   83 |        <strong>0.17 |       0.121 |</strong></p><p>----------------------------------------------------------------------------/</p><p>------------------------------------------------------------------------\</p><p>            UTR | total pred | CDS bnd. corr. |   meanDiff | medianDiff |</p><p>------------------------------------------------------------------------|</p><p>            TSS |         21 |              0 |         -1 |         -1 |</p><p>            TTS |          5 |              0 |         -1 |         -1 |</p><p>------------------------------------------------------------------------|</p><p>            UTR | uniq. pred |    unique anno |      sens. |      spec. |</p><p>------------------------------------------------------------------------|</p><p>                |  true positive = 1 bound. exact, 1 bound. &lt;= 20bp off |</p><p>UTR exon level |          0 |              0 |       -nan |       -nan |</p><p>------------------------------------------------------------------------|</p><p>UTR base level |          0 |              0 |       -nan |       -nan |</p><p>------------------------------------------------------------------------/</p></blockquote><p><em>this optomization/etraining appears to be giving diminishing returns—gene level stats are same as prior round</em></p><p>&nbsp;</p><h2><a name='header-n481' class='md-header-anchor '></a>PHASE 4</h2><p><u><strong>Run round 4 of MAKER (third <em>ab initio</em> run (i.e. SNAP round3, Augustus round2))</strong></u></p><p><strong>run maker</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="" contenteditable="false" cid="n484" mdtype="fences">&gt; mpiexec -n 30 tools/maker/bin/maker -base GopAga2_rnd4 rnd4-maker_opts.ctl 
maker_bopts.ctl maker_exe.ctl maker_evm.ctl &amp;&gt; Gopaga2_rnd4_10May2019.txt &amp;
</pre><blockquote><p>Choosing best annotations</p><p>processing chunk output</p><p>processing contig output</p><p>Start_time: 1557607146</p><p>End_time:   1557839922</p><p>Elapsed:    232776</p><p>Maker is now finished!!!</p></blockquote><p>&nbsp;</p><p><strong>merge into gff and fastas</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n495" mdtype="fences">&gt; /tools/maker/bin/gff3_merge -s -d GopAga2_rnd4_master_datastore_index.log &gt; GopAga2_rnd4.all.maker.gff
&gt; tools/maker/bin/gff3_merge -n -s -d GopAga2_rnd4_master_datastore_index.log &gt; GopAga2_rnd4.all.maker.noseq.gff
&gt; tools/maker/bin/fasta_merge -d GopAga2_rnd4_master_datastore_index.log
</pre><p>&nbsp;</p><p><strong>MAKER round 4 results</strong></p><p><strong># genes and lengths</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n499" mdtype="fences">&gt; cat GopAga2_rnd4.all.maker.noseq.gff | awk '{ if ($3 == "gene") print $0 }' | awk '{ sum += ($5 - $4) } END { print NR, sum / NR }'
</pre><blockquote><p>gene <span>	</span>  length</p><p><strong>25469 <span>	</span>21364.4*</strong></p></blockquote><p><em>we’ve converged on a similar number of genes and gene lengths</em></p><p>&nbsp;</p><p><strong>AED distribution</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n506" mdtype="fences">&gt; tools/maker/exe/Genome_annotation/AED_cdf_generator.pl -b 0.025 GopAga2_rnd4.all.maker.gff &gt; GopAga2_rnd4_AED_dis.out
</pre><blockquote><p><strong>AED     GopAga2_rnd4_nobusco.all.maker.gff</strong></p><p><strong>0.000   0.094</strong></p><p><strong>0.025   0.200</strong></p><p><strong>0.050   0.325</strong></p><p><strong>0.075   0.390</strong></p><p><strong>0.100   0.468</strong></p><p><strong>0.125   0.512</strong></p><p><strong>0.150   0.571</strong></p><p><strong>0.175   0.606</strong></p><p><strong>0.200   0.651</strong></p><p><strong>0.225   0.677</strong></p><p><strong>0.250   0.711</strong></p><p><strong>0.275   0.731</strong></p><p><strong>0.300   0.761</strong></p><p><strong>0.325   0.777</strong></p><p><strong>0.350   0.800</strong></p><p><strong>0.375   0.814</strong></p><p><strong>0.400   0.832</strong></p><p><strong>0.425   0.844</strong></p><p><strong>0.450   0.865</strong></p><p><strong>0.475   0.886</strong></p><p><strong>0.500   0.911</strong></p><p>0.525   0.916</p><p>0.550   0.923</p><p>0.575   0.928</p><p>0.600   0.934</p><p>0.625   0.937</p><p>0.650   0.943</p><p>0.675   0.946</p><p>0.700   0.952</p><p>0.725   0.955</p><p>0.750   0.959</p><p>0.775   0.962</p><p>0.800   0.968</p><p>0.825   0.971</p><p>0.850   0.977</p><p>0.875   0.980</p><p>0.900   0.985</p><p>0.925   0.988</p><p>0.950   0.993</p><p>0.975   0.996</p><p>1.000   1.000</p></blockquote><p><em>AED distribution is nearly identical to previous round. Goal was 95% with 0.5 or less, but will take this and move forward</em></p><p>&nbsp;</p><h2><a name='header-n552' class='md-header-anchor '></a>POST-PROCESSING OF FILES</h2><p><u><strong>we want to make a few modifications to the products so they’re easier to use downstream:</strong></p><p><strong>1. sort genome fasta by descending length</strong></p><p><strong>2. rename scaffolds (including in gffs) based on new naming)</strong></p><p><strong>3. make the gff, protein and transcript fastas more functional by putting the gene names in the gene/fasta headers</strong></u></p><p>&nbsp;</p><p><em>note the functional_fasta and functional_gff tools that come with Maker depend on wu-blast, which was bought out and is now ab-blast, which is free for an educational license</em></p><p>&nbsp;</p><p><strong>get uniprot-sprot proteins [uniprot_sprot.fasta.gz]</strong></p><p><em>release date of 5/8/2019</em></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="" contenteditable="false" cid="n562" mdtype="fences">&gt;wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
&gt; gunzip uniprot_sprot.fasta.gz
</pre><p>&nbsp;</p><p><strong>obtain ab-blast &amp; set up</strong></p><p>apply for license:  <a href='https://blast.advbiocomp.com/' target='_blank' class='url'>https://blast.advbiocomp.com/</a></p><p>download items. need to move license.xml (emailed separately) to be read by ab-blast</p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n567" mdtype="fences">&gt; cd ~
&gt; ls -a #see hidden files
&gt; sudo mkdir ~/.config/ab-blast #if you don't see an ab-blast folder under your user .config folder
&gt; sudo cp license.xml ~/.config/ab-blast/ #move the license wherever it is to the new folder
&gt; chmod 600 ~/.config/ab-blast/license.xml #needed to change permissions
</pre><p>&nbsp;</p><p><strong>make xdformat database from unitprot-sprot fasta</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n570" mdtype="fences">./xdformat -p -o uniprotsprot uniprot_sprot.fasta #run from ab-blaster folder
</pre><blockquote><p>XDFORMAT 3.0 [2019-01-04] [linux-x64 2019-01-05T00:01:56]</p><p>Start:  2019-05-29T11:17:09</p><p>XDF Output Database:  uniprotsprot</p><p>Alphabet:  NCBIstdaa.2</p><p>Input: &quot;uniprot_sprot.fasta&quot;</p><p>No. of sequences (letters) written:  560,118  (201,292,445)</p><p>Longest sequence written (in database):  35,213  (35,213)</p><p>Total cpu time:  1.12u 0.49s 1.61t   Elapsed:  00:00:02</p><p>End:  2019-05-29T11:17:11</p></blockquote><p><em>ran quick</em></p><p>&nbsp;</p><p><strong>run uniprot mapping to Maker proteins from last round of Maker (Maker rnd 4)</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n584" mdtype="fences">&gt; ./blastp uniprotsprot GopAga2_rnd4.all.maker.proteins.fasta cpus=28 mformat=2 &gt; gopaga2_rnd4_uniprotblast.txt
</pre><blockquote><p><em><strong>note, some warnings</strong></em></p><p>WARNING:  HSPs involving 60 database sequences were not reported due to the</p><p>          limiting value of parameter B = 250.</p><p>NOTE:  You may want to consider using a low-complexity sequence filter to</p><p>       reduce the number of spurious matches that may be appearing in the</p><p>       output.  See the filter option at</p><p>       <a href='https://blast.advbiocomp.com/doc/parameters.html#filter' target='_blank' class='url'>https://blast.advbiocomp.com/doc/parameters.html#filter</a>.</p><p>WARNING:  HSPs involving 163 database sequences were not reported due to the</p><p>          limiting value of parameter B = 250.</p><p>[...]</p></blockquote><p>since we’re only giving it proteins from Maker, masking low complexity regions shouldn’t be too much of an issue?</p><p><em>cpu usage was correct as assessed via htop</em></p><p>&nbsp;</p><p><strong>use Maker functional scripts to move the gene Id information to the fasta IDs</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n600" mdtype="fences">&gt;tools/maker/bin/maker_functional_fasta uniprot_sprot.fasta gopaga2_rnd4_uniprotblast.blast.out GopAga2_rnd4.all.maker.proteins.fasta &gt; gopAga2.0_all.maker.proteins.fasta

&gt;/tools/maker/bin/maker_functional_fasta uniprot_sprot.fasta gopaga2_rnd4_uniprotblast.blast.out GopAga2_rnd4.all.maker.transcripts.fasta &gt; gopAga2.0_all.maker.transcripts.fasta
</pre><p>&nbsp;</p><p><strong>same thing for gff files (adds gene ID info to gene lines)</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n603" mdtype="fences">&gt;/tools/maker/bin/maker_functional_gff uniprot_sprot.fasta gopaga2_rnd4_uniprotblast.blast.out GopAga2_rnd4.all.maker.gff &gt; gopAga2.0_all.gff

&gt; /tools/maker/bin/maker_functional_gff uniprot_sprot.fasta gopaga2_rnd4_uniprotblast.blast.out GopAga2_rnd4.all.maker.noseq.gff &gt; gopAga2.0_noseq.gff
</pre><p><em>note, each processing step takes only a few minutes</em></p><p>&nbsp;</p><h3><a name='header-n606' class='md-header-anchor '></a>SORTING/RENAMING</h3><hr /><p><em>note, this uses scripts from BBtools</em></p><p><strong>from bbmap folder</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n610" mdtype="fences">&gt; ./sortbyname.sh in=/scratch/rGopAga2_annotation/desert_tortoise_genome.fasta out=gopAga2.0_sorted.fa length=t descending=t
</pre><blockquote><p>java -ea -Xmx409834m -Xms409834m -cp /scratch/dolby/tools/bbmap/current/ sort.SortByName in=/scratch/rGopAga2_annotation/desert_tortoise_01Jun2017_CC6lQ_rename.fasta out=gopAga2.0_sorted.fa length=t descending=t</p><p>Executing sort.SortByName [in=/scratch/rGopAga2_annotation/desert_tortoise_01Jun2017_CC6lQ_rename.fasta, out=gopAga2.0_sorted.fa, length=t, descending=t]</p><p>Input is being processed as unpaired</p><p>Finished reading input.</p><p>Sorting.</p><p>Created a WriteThread for gopAga2.0_sorted.fa</p><p>Time:                             33.440 seconds.</p><p>Reads Processed:        161k     4.83k reads/sec</p><p>Bases Processed:       2338m     69.94m bases/sec</p></blockquote><p><em>headed file to confirm output</em> (order should change)</p><p>&nbsp;</p><p><strong>rename scaffolds</strong></p><p><em>note, it’s easier to do this at the start before you annotate the genome</em></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; ./rename.sh <span class="cm-def">in</span><span class="cm-operator">=</span>gopAga2.0_sorted.fa <span class="cm-def">out</span><span class="cm-operator">=</span>gopAga2.0_sorted.rename.fa <span class="cm-def">prefix</span><span class="cm-operator">=</span>scaffold</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 44px;"></div><div class="CodeMirror-gutters" style="display: none; height: 44px;"></div></div></div></pre><blockquote><p>java -ea -Xmx1g -cp /scratch/dolby/tools/bbmap/current/ jgi.RenameReads in=gopAga2.0_sorted.fa out=gopAga2.0_sorted.rename.fa prefix=scaffold</p><p>Executing jgi.RenameReads [in=gopAga2.0_sorted.fa, out=gopAga2.0_sorted.rename.fa, prefix=scaffold]</p><p>&nbsp;</p><p>Time: 21.297 seconds.</p></blockquote><p><em>head file again to confirm output</em></p><p>&nbsp;</p><p><strong>index files using samtools faidx, then use house script to make a name-mapping file</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n634" mdtype="fences">&gt; samtools faidx gopAga2.0_sorted.fa #makes .fai index file
&gt; samtools faidx gopAga2.0_sorted.rename.fa #makes .fai index file

&gt; python Associate_fasta_names.py --old gopAga2.0_sorted.fa.fai --old gopAga2.0_sorted.rename.fa.fai --out names.txt #makes names.txt file with associations
</pre><p>&nbsp;</p><p><strong>now rename the gff file based on this new naming scheme</strong></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n637" mdtype="fences">&gt; python Replace_name_maker.py --names names.txt --gff gopAga2.0_noseq.gff --out gopAga2.0_noseq.rename.gff
</pre><p>head file to confirm output:</p><blockquote><p>[gadolby@omega postprocess_maker_final]$  head -100 gopAga2.0_noseq.rename.gff</p><p>##gff-version 3</p><p>scaffold_185 . contig 1 702497 . . . ID=scaffold_185;Name=scaffold_185</p><p>scaffold_185 maker gene 94334 111982 . + . ID=maker-scaffold_185-augustus-gene-0.52;Name=maker-scaffold_185-augustus-gene-0.52;Note=Similar to BTN1A1: Butyrophilin subfamily 1 member A1 (Bos taurus OX%3D9913);</p><p>scaffold_185 maker mRNA 94334 111982 . + . ID=maker-scaffold_185-augustus-gene-0.52-mRNA-1;Parent=maker-scaffold_185-augustus-gene-0.52;Name=maker-scaffold_185-augustus-gene-0.52-mRNA-1;<em>AED=0.31;</em>eAED=0.31;_QI=209|0.5|0.85|0.85|0.5|0.57|7|1458|371;Note=Similar to BTN1A1: Butyrophilin subfamily 1 member A1 (Bos taurus OX%3D9913);</p><p>scaffold_185 maker exon 94334 94687 . + . ID=maker-scaffold_185-augustus-gene-0.52-mRNA-1:1;Parent=maker-scaffold_185-augustus-gene-0.52-mRNA-1</p><p>scaffold_185 maker exon 98174 98521 . + . ID=maker-scaffold_185-augustus-gene-0.52-mRNA-1:2;Parent=maker-scaffold_185-augustus-gene-0.52-mRNA-1</p></blockquote><p>&nbsp;</p><p>looks right!</p><p>&nbsp;</p><h3><a name='header-n652' class='md-header-anchor '></a>preparing final files</h3><p><strong>making a tidy version of the annotation (minus repeat regions)</strong></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 8px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-builtin">grep</span> <span class="cm-attribute">-Pv</span> <span class="cm-string">"\trepeat*"</span> gopAga2.0_noseq.rename.gff &gt; gopAga2.0_noseq.rename_tidy.gff</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; &nbsp;<span class="cm-builtin">grep</span> <span class="cm-attribute">-Pv</span> <span class="cm-string">"grep -Pv "</span>augustus_mask*|snap_mask*<span class="cm-string">" gopAga2.0_noseq.rename_tidy.gff &gt; gopAga2.0_noseq.rename_tidy2.gff</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 110px;"></div><div class="CodeMirror-gutters" style="display: none; height: 110px;"></div></div></div></pre><p>&nbsp;</p><h6><a name='header-n650' class='md-header-anchor '></a>##end</h6><p>&nbsp;</p></div>
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